Version Compatibility

Reference examples tested with: Cellpose 3.0+, anndata 0.10+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scvi-tools 1.1+, squidpy 1.3+, steinbock 0.16+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Imaging Mass Cytometry Pipeline

"Process my imaging mass cytometry data from images to spatial analysis" → Orchestrate image preprocessing (steinbock), cell segmentation (Cellpose), phenotyping (FlowSOM/scanpy), spatial neighborhood analysis (squidpy), and tissue community detection.

Pipeline Overview